This Company Is Using DNA to Sniff Out Contaminated Food

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This Company Is Using DNA to Sniff Out Contaminated Food

Clear Labs

Seeing the contents of the freezer at Clear Labs, you could be forgiven for thinking you'd stumbled into a college dorm room. Stacked high with Ziplocs, it's stocked with seemingly every frozen food known to man: microwaveable burgers, chicken bacon ranch sandwiches, mozzarella sticks. It's not all that different from a freezer at your typical Bay Area startup, actually—except this food isn't for eating. It's for analyzing.

Clear Labs is a food analytics company, and those stacks of frozen food are its ticket to the big time. For the past two years, the company has been collecting samples from markets in the United States and analyzing them to expand its genetic collection. Now the company claims it has the world's largest database of food genetic markers. And it wants to use that data to change how manufacturers manage the food supply.

For more than a decade, scientists have been using genetic markers like these, also called DNA barcodes, to identify tissue samples from plants, animals, or anything else with DNA. It's simpler than sequencing a whole genome: By looking at conserved gene regions that have mutated throughout evolutionary history, scientists can identify a species based on relatively few segments of DNA. One standard barcode region, for example, is a sequence of 648 base pairs within the gene for mitochondrial cytochrome c oxidase 1, or CO1. Every animal contains a version of the gene for CO1, a critical part of the electron transport chain that helps drive the synthesis of ATP—the fuel that runs your cells.

But throughout history, small mutations—a nucleotide here, a nucleotide there—accumulate in the gene, and it’s those tiny tweaks that allow scientists to tell whether the genetic segment came from a bird or a fish or a fly. Other genetic regions are better for distinguishing species within groups of plants, bacteria, or fungi.

Over time, researchers have accumulated those barcodes in big, public databases hosted by the National Center for Biotechnology Information or the Consortium for the Barcode of Life. Those two collections have far more total sequences than Clear Labs, but many of them aren’t food-specific; they’re mostly there for researchers to pull apart animal and plant taxonomies (you don’t see much red-bellied woodpecker in the food supply).

That's why Clear Labs decided it needed to build its own database—repeatedly sequencing the same species that show up in food products until it had a consistent description of the genetic markers within. The company won't say exactly how many food genetic markers it has, but it's confident it has more than any of the main databases, and it will continue to expand now that Clear Labs has launched its first product, Clear View, in private beta.

Clear View was built for food retailers and manufacturers who want to keep a close eye on the safety and integrity of their products. By identifying the species of plants, animals, bacteria, and fungi in a sample, they can suss out the authenticity of an ingredient (whether the fish in those fish sticks is really what you think it is). They can also tell if a food is contaminated by microbes, contains an allergen, or has certain genetically modified ingredients. (The company isn't taking a stand on whether the ingredients are good or bad—just whether they're there or not).

When a sample winds up at Clear Labs, its technicians extract DNA from a piece of food about half the size of a peanut, tens to hundreds of milligrams. Then they’ll amplify the DNA, using primers to isolate a few of those barcode regions. (For something like pizza with toppings, they’ll take multiple samples from the pepperoni and the cheese and the crust.) Depending on the food category, they’ll amplify three DNA barcode regions for plants, three for animals, two for bacteria, and two for fungi. Then they sequence those markers, compare them to the sequences in their reference database, and ping! there’s a match (or two or four).

Food companies have long been able to test their products for contamination with chemical tests. But "they're not nearly as specific as the DNA," says biologist Brent Mishler at UC Berkeley. And those tests typically look for one thing at a time—whether it’s gluten in a product marketed to people who suffer from celiac disease or bacterial contamination from Salmonella. DNA barcoding, though, is an agnostic test: It’ll pick up everything in a sample. Even if you just wanted to check to see whether your fish is albacore and not escolar, the markers used by Clear Labs would also pick up bacterial contamination if it happens to be there.

That agnosticism actually makes things cheaper. Because they can batch samples together, the tests are one to two orders of magnitude cheaper than existing tests, says CMO and co-founder Mahni Ghorashi. And Clear Labs is betting that with those cheaper tests, food manufacturers will test more and sooner. “It lets industry move from a reactive testing model, responding to outbreaks and recalls, to much more of a proactive model,” says Ghorashi. “They can sequence before these issues happen.”

The downside to DNA barcoding is that not everything has DNA—or DNA that can be sequenced. "If something’s been really cooked and heated, the DNA gets broken down into little pieces and it can’t be sequenced anymore," says Mishler. But manufacturers can address that problem by testing ingredients from their supply chain before it goes into their final products. And Clear Labs can integrate tests for non-living things like hormones, antibiotics, heavy metals, and pesticides into its barcoding system.

It’s possible that those tests soon won’t be an option—they’ll be a requirement. Just last week, the FDA finalized new rules that will require food manufacturers to create and execute detailed plans to prevent food contamination. That decision came in the wake of a rash of contamination problems in the food supply, notably a Listeria outbreak in ice cream that killed three people. Ghorashi says that 10 percent of the samples they've tested at Clear Labs has had some type of adulteration or contamination. If their tests get picked up, dorm room freezers the world 'round will be that much safer.